Align Inositol transport system ATP-binding protein (characterized)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein
Query= reanno::WCS417:GFF2332 (517 letters) >FitnessBrowser__Dyella79:N515DRAFT_2413 Length = 505 Score = 342 bits (878), Expect = 1e-98 Identities = 190/497 (38%), Positives = 294/497 (59%), Gaps = 7/497 (1%) Query: 21 PYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEI 80 P +L+ + K F +AL V L +R G V ALMG+NGAGKSTL+K++ G+ +PD G + Sbjct: 10 PVVLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGSV 69 Query: 81 RLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGR-EQLNSLHMVNHREMHR 139 L G+ I TP+ AQ+ GI ++QE+NL P++S+AEN++ GR + L M++ R++ Sbjct: 70 ELDGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRRRRLRMIDWRQVRD 129 Query: 140 CTAELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHL 199 LL +L + LD + +G+ +A RQMV IA+A+ + +LI+DEPTS++ E EV L Sbjct: 130 GARSLLRQLHLELDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVREL 189 Query: 200 FSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGR 259 F +IA L+ +G I+++TH +++V+A++D + V RDG +G + +L++ MVGR Sbjct: 190 FRVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPPAALVNAMVGR 249 Query: 260 ELSQL----FPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVA 315 +L + P + + L G V + GE+LG+ GL+GSGRT +A Sbjct: 250 DLPTVAGADAERAPPPDAPPAIDAQGLGCRGKLHPVDLQVRRGEMLGLGGLLGSGRTELA 309 Query: 316 ETIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAV 375 +FG+ + G++ + G+ V + P A+ +G AL E+RK G+ LSV EN+ +A+ Sbjct: 310 RLLFGLDRAERGELRIGGERVELKHPADAVVRGLALCPEERKTDGIVAELSVRENIVLAL 369 Query: 376 LPHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRL 435 G + + L + + L +K +E + LSGGNQQK +LARWL+T PRL Sbjct: 370 QARQGWRGMSRARQ-DELARQLVQALGIKAADIETPVGLLSGGNQQKVMLARWLVTEPRL 428 Query: 436 LILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGT 495 LILDEPTRGIDV AK E+ + A GMAV+ IS+E E+ DR+ VM E G Sbjct: 429 LILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWCDRIAVMRERRKAGE 488 Query: 496 LDRSEATQEKVMQLASG 512 L +T+ +V+ + +G Sbjct: 489 LP-GGSTEARVLAMIAG 504 Lambda K H 0.320 0.136 0.381 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 565 Number of extensions: 34 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 517 Length of database: 505 Length adjustment: 35 Effective length of query: 482 Effective length of database: 470 Effective search space: 226540 Effective search space used: 226540 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory